Learning representations for gene ontology terms by jointly encoding graph structure and textual node descriptors
Sign Up to like & getrecommendations! Published in 2022 at "Briefings in bioinformatics"
DOI: 10.1093/bib/bbac318
Abstract: Measuring the semantic similarity between Gene Ontology (GO) terms is a fundamental step in numerous functional bioinformatics applications. To fully exploit the metadata of GO terms, word embedding-based methods have been proposed recently to map… read more here.
Keywords: structure; encoding graph; ontology; gene ontology ... See more keywords
SANA NetGO: a combinatorial approach to using Gene Ontology (GO) terms to score network alignments
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DOI: 10.1093/bioinformatics/btx716
Abstract: Motivation Gene Ontology (GO) terms are frequently used to score alignments between protein‐protein interaction (PPI) networks. Methods exist to measure GO similarity between proteins in isolation, but proteins in a network alignment are not isolated:… read more here.
Keywords: ontology; network; measure; ontology terms ... See more keywords
TreeGrafter: phylogenetic tree-based annotation of proteins with Gene Ontology terms and other annotations
Sign Up to like & getrecommendations! Published in 2019 at "Bioinformatics"
DOI: 10.1093/bioinformatics/bty625
Abstract: Summary TreeGrafter is a new software tool for annotating protein sequences using pre‐annotated phylogenetic trees. Currently, the tool provides annotations to Gene Ontology (GO) terms, and PANTHER family and subfamily. The approach is generalizable to… read more here.
Keywords: ontology; tree; ontology terms; gene ontology ... See more keywords